A multidisciplinary approach reveals a new species of glassfrog from Colombia (Anura: Centrolenidae: Nymphargus)

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Abstract

Anurans of the family Centrolenidae are a highly diverse clade of Neotropical treefrogs. In the last two decades, glassfrogs have become a model system for studies in ecology and evolutionary biology, in part because their taxonomy and phylogenetic relationships are considered relatively well established. However, there are still many gaps in our knowledge, for example, which morphological characters are important for species delimitation. Consequently, several species complexes in Centrolenidae remain unresolved. Using data on external and internal morphology of adult individuals, tadpoles, advertisement call traits and genetic sequences, we describe a new species of glassfrog (Nymphargus pijao sp. nov.) endemic to Colombia that has been previously missasigned to Nymphargus griffithsi. We include in this description data of three phenotypic characters related to pectoral musculature and testis size, which have been traditionally overlooked in studies about the taxonomy and systematics of glassfrogs. In addition, we present details of a low-cost method implemented in the field to rear tadpoles of the new species. This methodology can solve common problems during the management and care of glassfrogs egg masses and tadpoles, and hence, promotes their description for more species and a better knowledge of the anuran biodiversity in Neotropics.

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MUSCLE: multiple sequence alignment with high accuracy and high throughput.

R. C. Edgar (2004)

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.

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AliView: a fast and lightweight alignment viewer and editor for large datasets

Anders Larsson (2014)

Summary: AliView is an alignment viewer and editor designed to meet the requirements of next-generation sequencing era phylogenetic datasets. AliView handles alignments of unlimited size in the formats most commonly used, i.e. FASTA, Phylip, Nexus, Clustal and MSF. The intuitive graphical interface makes it easy to inspect, sort, delete, merge and realign sequences as part of the manual filtering process of large datasets. AliView also works as an easy-to-use alignment editor for small as well as large datasets. Availability and implementation: AliView is released as open-source software under the GNU General Public License, version 3.0 (GPLv3), and is available at GitHub (www.github.com/AliView). The program is cross-platform and extensively tested on Linux, Mac OS X and Windows systems. Downloads and help are available at http://ormbunkar.se/aliview Contact: anders.larsson@ebc.uu.se Supplementary information: Supplementary data are available at Bioinformatics online.

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TNT version 1.5, including a full implementation of phylogenetic morphometrics

Pablo Goloboff, Santiago A. Catalano (2016)

Version 1.5 of the computer program TNT completely integrates landmark data into phylogenetic analysis. Landmark data consist of coordinates (in two or three dimensions) for the terminal taxa; TNT reconstructs shapes for the internal nodes such that the difference between ancestor and descendant shapes for all tree branches sums up to a minimum; this sum is used as tree score. Landmark data can be analysed alone or in combination with standard characters; all the applicable commands and options in TNT can be used transparently after reading a landmark data set. The program continues implementing all the types of analyses in former versions, including discrete and continuous characters (which can now be read at any scale, and automatically rescaled by TNT). Using algorithms described in this paper, searches for landmark data can be made tens to hundreds of times faster than it was possible before (from T to 3T times faster, where T is the number of taxa), thus making phylogenetic analysis of landmarks feasible even on standard personal computers.